Variant report

Variant	rs16970170
Chromosome Location	chr15:74868100-74868101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74860211..74862680-chr15:74866308..74868152,2	MCF-7	breast:
2	chr15:74867427..74869520-chr15:74870495..74873401,2	MCF-7	breast:
3	chr15:74867157..74869527-chr15:74870392..74871994,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11629492	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11631682	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs11632086	0.82[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633208	0.84[EUR][1000 genomes]
rs11633539	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs11633697	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634261	1.00[AMR][1000 genomes]
rs11637129	1.00[EUR][1000 genomes]
rs16970078	1.00[ASW][hapmap];1.00[LWK][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes]
rs16972511	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs17343071	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17861094	0.82[AFR][1000 genomes]
rs2069519	0.82[ASW][hapmap]
rs2069521	0.91[YRI][hapmap]
rs2069522	0.82[ASW][hapmap]
rs2069525	0.82[ASW][hapmap]
rs2069526	0.82[ASW][hapmap]
rs4646427	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs57317343	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57592570	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60130631	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74025819	0.80[AFR][1000 genomes]
rs74025821	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16970170	SCAMP5	cis	lymphoblastoid	seeQTL
rs16970170	CEP170	trans	brain	seeQTL
rs16970170	SCAMP5	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74839400-74880600	Weak transcription	Hela-S3	cervix
2	chr15:74840600-74890400	Weak transcription	Stomach Mucosa	stomach
3	chr15:74845400-74880200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:74845600-74876200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:74845800-74890400	Weak transcription	A549	lung
6	chr15:74851200-74875400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:74851800-74887800	Strong transcription	GM12878-XiMat	blood
8	chr15:74854800-74888600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:74856600-74872400	Weak transcription	K562	blood
10	chr15:74857600-74888200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:74857800-74876600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:74857800-74887600	Strong transcription	Primary T cells from cord blood	blood
13	chr15:74859000-74888600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:74859200-74871800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:74859400-74874400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:74859400-74879200	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr15:74859600-74888000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:74859800-74873600	Strong transcription	Fetal Thymus	thymus
19	chr15:74860000-74875200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:74860400-74877800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:74860400-74889000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:74860600-74880200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr15:74860800-74888400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:74861000-74875200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:74861200-74871800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:74861200-74889800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:74861400-74876200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:74861600-74874000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:74861800-74869400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr15:74861800-74870400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:74861800-74871800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr15:74861800-74871800	Strong transcription	Thymus	Thymus
33	chr15:74861800-74873400	Strong transcription	Lung	lung
34	chr15:74861800-74874800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:74861800-74879200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:74862000-74869400	Strong transcription	Liver	Liver
37	chr15:74862000-74869600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:74862000-74873800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:74862800-74871400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:74863000-74875200	Strong transcription	Primary B cells from cord blood	blood
41	chr15:74863200-74876400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:74863200-74880600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:74863200-74880800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:74863400-74880600	Weak transcription	NHLF	lung
45	chr15:74863600-74890800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr15:74863800-74872000	Strong transcription	Adipose Nuclei	Adipose
47	chr15:74863800-74880200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:74863800-74882200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:74863800-74890400	Weak transcription	Psoas Muscle	Psoas
50	chr15:74864000-74876000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links